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Genbank parser doesn't handle feature attributes with colliding names.

Open TimothyStiles opened this issue 2 years ago • 5 comments

Describe the bug

The genbank parser cannot handle repeating attribute keys like with /db_xref below:

Screen Shot 2023-10-06 at 2 01 30 PM

Severity of the bug

This is blocking Ark's ability to cross reference other databases. (priority)

Steps to reproduce

You can debug this by debugging BenchmarkRead(b *testing.B){} in genbank_test.go within a couple of feature extraction loops you'll see that db_xref only keeps the last reference.

Expected behavior

We need to be able to track attributes with the same key name. List of tuples?

Screenshots

Screen Shot 2023-10-06 at 3 39 43 PM

Client information

  • OS: Mac OSX 0.15.7
  • Golang version: 1.21
  • poly version v0.27.1

TimothyStiles avatar Oct 06 '23 23:10 TimothyStiles

adding @Koeng101 to the issue.

TimothyStiles avatar Oct 06 '23 23:10 TimothyStiles

This issue has had no activity in the past 2 months. Marking as stale.

github-actions[bot] avatar Dec 06 '23 18:12 github-actions[bot]

Working on this now!

carreter avatar Dec 12 '23 03:12 carreter

This should be an easy fix, but the entire genbank parser needs to be reworked, and it seems like it won't be trivial. I'll open a separate issue.

carreter avatar Dec 12 '23 04:12 carreter

This issue has had no activity in the past 2 months. Marking as stale.

github-actions[bot] avatar Feb 10 '24 18:02 github-actions[bot]